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"); document.write("
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"); document.write("
Multi-manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics.
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Brief. Bioinform. 26:bbaf162 (2025)
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Grexa,\ I.*\ ; Iván,\ Z.Z.*\ ; Migh,\ E.*\ ; Kovács,\ F.*\ ; Bolck,\ H.A.*\ ; Zheng,\ X.*\ ; Mund,\ A.*\ ; Moshkov,\ N.*\ ; Miczán,\ V.*\ ; Koos,\ K.*\ ; Horvath,\ P.
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SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy.
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Brief. Bioinform. 25:bbae029 (2024)
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Heylen,\ D.*\ ; Pusparum,\ M.*\ ; Kuliesius,\ J.*\ ; Wilson,\ J.*\ ; Park,\ Y.-C.\ ; Jamiołkowski,\ J.*\ ; D\'Onofrio,\ V.*\ ; Valkenborg,\ D.*\ ; Aerts,\ J.*\ ; Ertaylan,\ G.*\ ; Hooyberghs,\ J.*
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Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison.
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Brief. Bioinform. 26:bbae657 (2024)
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Zahedi,\ R.P.*\ ; Ghamsari,\ R.*\ ; Argha,\ A.*\ ; Macphillamy,\ C.*\ ; Beheshti,\ A.*\ ; Alizadehsani,\ R.*\ ; Lovell,\ N.H.*\ ; Lotfollahi,\ M.\ ; Alinejad-Rokny,\ H.*
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Deep learning in spatially resolved transcriptfomics: A comprehensive technical view.
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Brief. Bioinform. 25:bbae082 (2024)
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Henao,\ J.\ ; Lauber,\ M.*\ ; Azevedo,\ M.\ ; Grekova,\ A.\ ; Theis,\ F.J.\ ; List,\ M.*\ ; Ogris,\ C.\ ; Schubert,\ B.
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Multi-omics regulatory network inference in the presence of missing data.
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Brief. Bioinform. 24:13 (2023)
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Horlacher,\ M.\ ; Cantini,\ G.\ ; Hesse,\ J.\ ; Schinke,\ P.\ ; Goedert,\ N.\ ; Londhe,\ S.\ ; Moyon,\ L.\ ; Marsico,\ A.
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A systematic benchmark of machine learning methods for protein-RNA interaction prediction.
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Brief. Bioinform. 24:bbad307 (2023)
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Wang,\ J.*\ ; Horlacher,\ M.\ ; Cheng,\ L.*\ ; Winther,\ O.*
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RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies.
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Brief. Bioinform. 24:14 (2023)
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Han,\ S.\ ; Huang,\ J.\ ; Foppiano,\ F.\ ; Prehn,\ C.\ ; Adamski,\ J.*\ ; Suhre,\ K.*\ ; Li,\ Y.*\ ; Matullo,\ G.*\ ; Schliess,\ F.*\ ; Gieger,\ C.\ ; Peters,\ A.\ ; Wang-Sattler,\ R.
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TIGER: Technical variation elimination for metabolomics data using ensemble learning architecture.
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Brief. Bioinform. 23:bbab535 (2022)
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Jeong,\ Y.*\ ; Barros De Andrade E Sousa,\ L.\ ; Thalmeier,\ D.\ ; Toth,\ R.*\ ; Ganslmeier,\ M.*\ ; Breuer,\ K.*\ ; Plass,\ C.*\ ; Lutsik,\ P.*
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Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes.
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Brief. Bioinform. 23:bbac248 (2022)
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Villaverde,\ A.F.*\ ; Pathirana,\ D.*\ ; Fröhlich,\ F.\ ; Hasenauer,\ J.*\ ; Banga,\ J.R.*
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A protocol for dynamic model calibration.
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Brief. Bioinform. 23:bbab387 (2022)
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Deutelmoser,\ H.*\ ; Scherer,\ D.*\ ; Brenner,\ H.*\ ; Waldenberger,\ M.\ ; Suhre,\ K.*\ ; Kastenmüller,\ G.\ ; Lorenzo Bermejo,\ J.*
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Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data.
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Brief. Bioinform. 22:bbaa230 (2021)
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Peschel,\ S.\ ; Müller,\ C.L.\ ; von Mutius,\ E.\ ; Boulesteix,\ A.L.*\ ; Depner,\ M.
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NetCoMi: Network construction and comparison for microbiome data in R.
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Brief. Bioinform. 22, DOI: 10.1093/bib/bbaa290 (2021)
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Guala,\ D.*\ ; Ogris,\ C.\ ; Müller,\ N.S.\ ; Sonnhammer,\ E.L.L.*
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Genome-wide functional association networks: Background, data \& state-of-the-art resources.
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Brief. Bioinform. 21, 1224-1237 (2020)
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Hoksza,\ D.*\ ; Gawron,\ P.*\ ; Ostaszewski,\ M.*\ ; Hasenauer,\ J.\ ; Schneider,\ R.*
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Closing the gap between formats for storing layout information in systems biology.
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Brief. Bioinform. 21, 1249-1260 (2020)
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Hoksza,\ D.*\ ; Gawron,\ P.*\ ; Ostaszewski,\ M.*\ ; Hasenauer,\ J.\ ; Schneider,\ R.*
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Closing the gap between formats for storing layout information in systems biology.
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Brief. Bioinform. 22, 608 (2020)
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Omony,\ J.\ ; Nussbaumer,\ T.\ ; Gutzat,\ R.*
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DNA methylation analysis in plants: review of computational tools and future perspectives.
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Brief. Bioinform. 21, 906-918 (2020)
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Pitea,\ A.\ ; Kondofersky,\ I.*\ ; Sass,\ S.\ ; Theis,\ F.J.\ ; Müller,\ N.S.\ ; Unger,\ K.
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Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?
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Brief. Bioinform. 21, 272-281 (2020)
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Ostaszewski,\ M.*\ ; Gebel,\ S.*\ ; Kuperstein,\ I.*\ ; Mazein,\ A.*\ ; Zinovyev,\ A.*\ ; Dogrusoz,\ U.*\ ; Hasenauer,\ J.\ ; Fleming,\ R.M.T.*\ ; Le Novère,\ N.*\ ; Gawron,\ P.*\ ; Ligon,\ T.*\ ; Niarakis,\ A.*\ ; Nickerson,\ D.A.*\ ; Weindl,\ D.\ ; Balling,\ R.*\ ; Barillot,\ E.*\ ; Auffray,\ C.*\ ; Schneider,\ R.*
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Community-driven roadmap for integrated disease maps.
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Brief. Bioinform. 20, 659-670 (2019)
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Villmann,\ T.*\ ; Schleif,\ F.M.*\ ; Kostrzewa,\ M.*\ ; Walch,\ A.K.\ ; Hammer,\ B.*
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Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods.
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Brief. Bioinform. 9, 129-143 (2008)
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Yuille,\ M.*\ ; van Ommen,\ G.J.*\ ; Bréchot,\ C.*\ ; Cambon-Thomsen,\ A.*\ ; Dagher,\ G.*\ ; Landegren,\ U.*\ ; Litton,\ J.E.*\ ; Pasterk,\ M.*\ ; Peltonen,\ L.*\ ; Taussig,\ M.*\ ; Wichmann,\ H.-E.\ ; Zatloukal,\ K.*
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Biobanking for Europe.
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Brief. Bioinform. 9, 14-24 (2008)
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Mueller,\ J.C.
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Linkage disequilibrium for different scales and applications.
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Brief. Bioinform. 5, 1-10 (2004)
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Werner,\ T.
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The state of the art of mammalian promoter recognition.
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Brief. Bioinform. 4, 22-30 (2003)
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Hrabě de Angelis,\ M.\ ; Strivens,\ M.*
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Large-scale production of mouse phenotypes : the search for animal models for inherited diseases in humans.
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Brief. Bioinform. 2, 170-180 (2001)
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Werner,\ T.
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Identification and functional modelling of DNA sequence elements of transcription.
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Brief. Bioinform. 1, 372-380 (2000)
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